Method for identifying transplant donors for a transplant recipient

Abstract

The present disclosure relates to a method for identifying one or more potential transplant donors for a recipient in need of a transplant, the method comprising: generating a gene dosage map for each locus of a gene complex for the one or more potential donors and the recipient; comparing the gene dosage maps of the one or more potential donors and the recipient; and determining one or more transplant donors as a transplant match for a recipient in need of a transplant if the gene dosage map of the one or more transplant donors correlates with the gene dosage map of the recipient in need of a transplant; wherein the closer the correlation between the gene dosage maps of the one or more donors compared to the recipient, the higher the probability of the one or more donors being a transplant match and/or best transplant match for the recipient.

1 .- 56 . (canceled) 
     
     
         57 . A computer-implemented method for identifying one or more potential transplant donors for a recipient in need of a transplant, the method comprising:
 a) generating a gene dosage map, using a computer, for each locus of a gene complex for the one or more potential donors and the recipient based on loci-assigned sequences;   b) comparing the gene dosage maps of the one or more potential donors and the recipient, using a computer; and   c) determining one or more transplant donors as a transplant match for a recipient in need of a transplant if the gene dosage map of the one or more transplant donors correlates with the gene dosage map of the recipient in need of a transplant, using a computer;   
       wherein the closer the correlation between the gene dosage maps of the one or more donors compared to the recipient, the higher the probability of the one or more donors being a transplant match and/or best transplant match for the recipient. 
     
     
         58 . A computer-implemented method for identifying one or more potential transplant donors for a recipient in need of a transplant, the method comprising:
 a) generating sequences of a gene complex, using a computer, from a nucleic acid sample obtained from the one or more potential transplant donors and the recipient;   b) assigning a plurality of the sequences generated in step (a) corresponding to each locus of the gene complex, using a computer;   c) determining gene dosage for each locus of the gene complex from the plurality of sequences assigned in step (b), using a computer;   d) generating a gene dosage map of the gene complex for the one or more potential transplant donors and the recipient from the gene dosage for each of the locus of the gene complex determined in step (c), using a computer; and   e) comparing the generated gene dosage map of the one or more potential transplant donors with the generated gene dosage map of the recipient, using a computer;   wherein the one or more potential transplant donors is identified as a transplant match and/or best transplant match for a recipient in need of a transplant if the gene dosage map of the one or more transplant donors correlates with the gene dosage map of the recipient.   
     
     
         59 . A computer-implemented method for reducing the likelihood of a transplant recipient developing graft versus host disease (GVHD), the method comprising:
 a) generating sequences of a gene complex, using a computer, from a nucleic acid sample obtained from the one or more potential transplant donors and the recipient;   b) assigning a plurality of the sequences generated in step (a) corresponding to each locus of the gene complex, using a computer;   c) determining gene dosage for each locus of the gene complex from the plurality of sequences assigned in step (b), using a computer;   d) generating a gene dosage map of the gene complex for the one or more potential transplant donors and the recipient from the gene dosage for each locus of the gene complex determined in step (c), using a computer; and   e) comparing the generated gene dosage map of the one or more potential transplant donors with the generated gene dosage map of the recipient, using a computer;   wherein the gene dosage map of the one or more potential transplant donors correlating with the gene dosage map of the recipient in need of a transplant is indicative of reduced likelihood of the transplant recipient developing graft versus host disease following transplantation of a graft from the one or more transplant donors.   
     
     
         60 . A computer-implemented method for analysing sequences to identify one or more potential transplant donors for a recipient in need of a transplant, the method comprising:
 a) generating sequences of a gene complex, using a computer, from a nucleic acid sample obtained from the one or more potential transplant donors and the recipient;   b) assigning a plurality of the sequences generated in step (a) corresponding to each locus of the gene complex, using a computer;   c) determining gene dosage for each locus of the gene complex from the plurality of sequences assigned in step (b), using a computer;   d) generating a gene dosage map of the gene complex for the one or more potential transplant donors and the recipient from the gene dosage for each of the locus of the gene complex determined in step (c), using a computer; and   e) comparing the generated gene dosage map of the one or more potential transplant donors with the generated gene dosage map of the recipient, using a computer;   wherein the one or more potential transplant donors is identified as a transplant match and/or best transplant match for a recipient in need of a transplant, if the gene dosage map of the one or more transplant donors correlates with the gene dosage map of the recipient.   
     
     
         61 . A computer-implemented method of preventing graft versus host disease (GVHD) disease between one or more potential transplant donors and a recipient comprising
 a) generating sequences of a gene complex, using a computer, from a nucleic acid sample obtained from the one or more potential transplant donors and the recipient;   b) assigning a plurality of the sequences generated in step (a) corresponding to each locus of the gene complex, using a computer;   c) determining gene dosage for each locus of the gene complex from the plurality of sequences assigned in step (b), using a computer;   d) generating a gene dosage map of the gene complex for the one or more potential transplant donors and the recipient from the gene dosage for each locus of the gene complex determined in step (c), using a computer; and   e) comparing the generated gene dosage map of the one or more potential transplant donors with the generated gene dosage map of the recipient, using a computer;   wherein the gene dosage map of the one or more potential transplant donors correlating with the gene dosage map of the recipient in need of a transplant is indicative of reduced likelihood of the transplant recipient developing graft versus host disease following transplantation of a graft and/or tissue and/or organ from the one or more transplant donors, and   selecting graft and/or tissue and/or organ from a transplant donor having a gene dosage map that correlates with the gene dosage map of the recipient for transplant to the recipient.   
     
     
         62 . The computer-implemented method of  claim 58 , wherein generating the gene dosage map for each locus of the gene complex for the one or more potential donors and the recipient comprises dividing the plurality of sequences assigned to each locus by the plurality of sequences assigned to all loci of the gene complex. 
     
     
         63 . The computer-implemented method of  claim 57 , wherein the gene dosage for each locus is copy number for each locus, or all loci, of the gene complex. 
     
     
         64 . The computer-implemented method of  claim 63 , wherein the copy number for each locus and all loci of the gene complex allows determination of zygosity for each locus and all loci of the gene complex. 
     
     
         65 . The computer-implemented method of  claim 63 , wherein the copy number of each locus and all loci of the gene complex allows determination of whether two alleles have an identical sequence. 
     
     
         66 . The computer-implemented method of  claim 57 , wherein the gene complex is a highly polymorphic gene complex. 
     
     
         67 . The computer-implemented method of  claim 57 , wherein the gene complex is a gene complex pertaining to transplantation. 
     
     
         68 . The computer-implemented method of  claim 57 , wherein the gene complex is an HLA gene complex. 
     
     
         69 . The computer-implemented method of  claim 58 , wherein the step (b) of assigning a plurality of the sequences generated in step (a) corresponding to each locus of the gene complex is based on: one or more regions of each locus; all exons in each locus; and/or an entire sequence of each locus. 
     
     
         70 . The computer-implemented method of  claim 58 , wherein step (b) comprises assigning a plurality of the sequences generated in step (a) using a computer program. 
     
     
         71 . The computer-implemented method of  claim 70 , wherein the computer program is a sequence editing and alignment program. 
     
     
         72 . The computer-implemented method of  claim 58 , wherein the step of a) generating sequences of a gene complex, using a computer, from a nucleic acid sample obtained from the one or more potential transplant donors and the recipient comprises:
 a) contacting a nucleic acid sample from the one or more transplant donors and the recipient with oligonucleotide probes, wherein the oligonucleotide probes hybridize togene target sequences in the nucleic acid sample;   b) enriching a nucleic acid by hybridizing the nucleic acid to one or more oligonucleotide probes;   c) separating nucleic acid hybridized to the one or more oligonucleotide probes from nucleic acid not hybridized to the one or more oligonucleotide probes; and   d) sequencing the enriched nucleic acid to identify one or more gene alleles;   
       wherein the gene target sequences are in a non-coding region of the gene. 
     
     
         73 . The computer-implemented method of  claim 72 , wherein the gene complex is a highly polymorphic gene complex. 
     
     
         74 . The computer-implemented method of  claim 72 , wherein the gene complex is a gene complex pertaining to transplantation. 
     
     
         75 . The computer-implemented method of  claim 72 , wherein the gene complex is an HLA gene complex. 
     
     
         76 . The computer-implemented method of  claim 72 , wherein the method comprises amplifying the nucleic acid bound to the one or more oligonucleotide probes. 
     
     
         77 . The computer-implemented method of  claim 72 , wherein the method comprises sequencing an HLA gene exon, or a gene exon pertaining to transplantation. 
     
     
         78 . The computer-implemented method of  claim 72 , wherein the method comprises sequencing an entire HLA gene complex, or any entire gene complex pertaining to transplantation. 
     
     
         79 . The computer-implemented method of  claim 72 , wherein the one or more oligonucleotide probes comprises a capture tag. 
     
     
         80 . The computer-implemented method of  claim 79 , wherein the capture tag is biotin or streptavidin. 
     
     
         81 . The computer-implemented method of  claim 79 , wherein the method further comprises contacting the capture tag with a binding agent. 
     
     
         82 . The computer-implemented method of  claim 81 , wherein the binding agent is biotin or streptavidin. 
     
     
         83 . The computer-implemented method of  claim 72 , wherein the nucleic acid sample from the one or more transplant donors and the recipient in need of a transplant that is contacted with the one or more oligonucleotide probes comprises single stranded nucleic acid. 
     
     
         84 . The computer-implemented method of  claim 72 , wherein the nucleic acid sample is fragmented before or after being contacted with the one or more oligonucleotide probes. 
     
     
         85 . The computer-implemented method of  claim 84 , wherein the fragments of the nucleic acid sample have an average length greater than about 100 bp. 
     
     
         86 . The computer-implemented method of  claim 57 , wherein the nucleic acid sample from the one or more transplant donors and the recipient in need of a transplant is genomic DNA extracted from a biological sample. 
     
     
         87 . The computer-implemented method of  claim 86 , wherein the biological sample is whole blood. 
     
     
         88 . The computer-implemented method of  claim 86 , wherein the genomic DNA is at a concentration of about 10 ng/μl to about 100 ng/μl. 
     
     
         89 . The computer-implemented method of  claim 72 , wherein sequencing is performed using high-throughput sequencing. 
     
     
         90 . The computer-implemented method of  claim 89 , wherein the high-throughput sequencing is hybrid-capture next generation sequencing. 
     
     
         91 . The computer-implemented method of  claim 58 , wherein the sequences are generated in a computer readable form. 
     
     
         92 . The computer-implemented method of  claim 91 , wherein the computer readable form is FASTQ.